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Iron in PDB 7u5l: Cryo-Em Structure of Ferritin

Enzymatic activity of Cryo-Em Structure of Ferritin

All present enzymatic activity of Cryo-Em Structure of Ferritin:
1.16.3.1;

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure of Ferritin (pdb code 7u5l). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Cryo-Em Structure of Ferritin, PDB code: 7u5l:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in 7u5l

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Iron binding site 1 out of 24 in the Cryo-Em Structure of Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:75.0
occ:1.00
 ND1 A:HIS66 1.7 62.8 1.0
OE1 A:GLU63 2.1 63.5 1.0
OE2 A:GLU28 2.4 60.1 1.0
CE1 A:HIS66 2.5 62.8 1.0
CG A:HIS66 2.9 62.8 1.0
CD A:GLU63 2.9 63.5 1.0
CD A:GLU28 3.2 60.1 1.0
OE1 A:GLU28 3.2 60.1 1.0
OE2 A:GLU63 3.3 63.5 1.0
CB A:HIS66 3.5 62.8 1.0
NE2 A:HIS66 3.6 62.8 1.0
CD2 A:HIS66 3.8 62.8 1.0
NE2 A:GLN142 3.9 59.9 1.0
CA A:GLU63 4.2 63.5 1.0
CG A:GLU63 4.2 63.5 1.0
CB A:GLU63 4.3 63.5 1.0
CG A:GLU28 4.6 60.1 1.0
CG1 A:VAL111 4.6 58.8 1.0
N A:GLU63 4.9 63.5 1.0
CD A:GLN142 4.9 59.9 1.0
O A:GLU63 4.9 63.5 1.0
CA A:HIS66 4.9 62.8 1.0

Iron binding site 2 out of 24 in 7u5l

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Iron binding site 2 out of 24 in the Cryo-Em Structure of Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:75.0
occ:1.00
 ND1 B:HIS66 1.7 62.8 1.0
OE1 B:GLU63 2.1 63.5 1.0
OE2 B:GLU28 2.4 60.1 1.0
CE1 B:HIS66 2.5 62.8 1.0
CG B:HIS66 2.9 62.8 1.0
CD B:GLU63 2.9 63.5 1.0
CD B:GLU28 3.2 60.1 1.0
OE1 B:GLU28 3.2 60.1 1.0
OE2 B:GLU63 3.3 63.5 1.0
CB B:HIS66 3.5 62.8 1.0
NE2 B:HIS66 3.6 62.8 1.0
CD2 B:HIS66 3.8 62.8 1.0
NE2 B:GLN142 3.9 59.9 1.0
CA B:GLU63 4.2 63.5 1.0
CG B:GLU63 4.2 63.5 1.0
CB B:GLU63 4.3 63.5 1.0
CG B:GLU28 4.6 60.1 1.0
CG1 B:VAL111 4.6 58.8 1.0
N B:GLU63 4.9 63.5 1.0
CD B:GLN142 4.9 59.9 1.0
O B:GLU63 4.9 63.5 1.0
CA B:HIS66 4.9 62.8 1.0

Iron binding site 3 out of 24 in 7u5l

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Iron binding site 3 out of 24 in the Cryo-Em Structure of Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:75.0
occ:1.00
 ND1 C:HIS66 1.7 62.8 1.0
OE1 C:GLU63 2.1 63.5 1.0
OE2 C:GLU28 2.4 60.1 1.0
CE1 C:HIS66 2.5 62.8 1.0
CG C:HIS66 2.9 62.8 1.0
CD C:GLU63 2.9 63.5 1.0
CD C:GLU28 3.2 60.1 1.0
OE1 C:GLU28 3.2 60.1 1.0
OE2 C:GLU63 3.3 63.5 1.0
CB C:HIS66 3.5 62.8 1.0
NE2 C:HIS66 3.6 62.8 1.0
CD2 C:HIS66 3.8 62.8 1.0
NE2 C:GLN142 3.9 59.9 1.0
CA C:GLU63 4.2 63.5 1.0
CG C:GLU63 4.2 63.5 1.0
CB C:GLU63 4.3 63.5 1.0
CG C:GLU28 4.6 60.1 1.0
CG1 C:VAL111 4.6 58.8 1.0
N C:GLU63 4.9 63.5 1.0
CD C:GLN142 4.9 59.9 1.0
O C:GLU63 4.9 63.5 1.0
CA C:HIS66 4.9 62.8 1.0

Iron binding site 4 out of 24 in 7u5l

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Iron binding site 4 out of 24 in the Cryo-Em Structure of Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:75.0
occ:1.00
 ND1 D:HIS66 1.7 62.8 1.0
OE1 D:GLU63 2.1 63.5 1.0
OE2 D:GLU28 2.4 60.1 1.0
CE1 D:HIS66 2.5 62.8 1.0
CG D:HIS66 2.9 62.8 1.0
CD D:GLU63 2.9 63.5 1.0
CD D:GLU28 3.2 60.1 1.0
OE1 D:GLU28 3.2 60.1 1.0
OE2 D:GLU63 3.3 63.5 1.0
CB D:HIS66 3.5 62.8 1.0
NE2 D:HIS66 3.6 62.8 1.0
CD2 D:HIS66 3.8 62.8 1.0
NE2 D:GLN142 3.9 59.9 1.0
CA D:GLU63 4.2 63.5 1.0
CG D:GLU63 4.2 63.5 1.0
CB D:GLU63 4.3 63.5 1.0
CG D:GLU28 4.6 60.1 1.0
CG1 D:VAL111 4.6 58.8 1.0
N D:GLU63 4.9 63.5 1.0
CD D:GLN142 4.9 59.9 1.0
O D:GLU63 4.9 63.5 1.0
CA D:HIS66 4.9 62.8 1.0

Iron binding site 5 out of 24 in 7u5l

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Iron binding site 5 out of 24 in the Cryo-Em Structure of Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em Structure of Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:75.0
occ:1.00
 ND1 E:HIS66 1.7 62.8 1.0
OE1 E:GLU63 2.1 63.5 1.0
OE2 E:GLU28 2.4 60.1 1.0
CE1 E:HIS66 2.5 62.8 1.0
CG E:HIS66 2.9 62.8 1.0
CD E:GLU63 2.9 63.5 1.0
CD E:GLU28 3.2 60.1 1.0
OE1 E:GLU28 3.2 60.1 1.0
OE2 E:GLU63 3.3 63.5 1.0
CB E:HIS66 3.5 62.8 1.0
NE2 E:HIS66 3.6 62.8 1.0
CD2 E:HIS66 3.8 62.8 1.0
NE2 E:GLN142 3.9 59.9 1.0
CA E:GLU63 4.2 63.5 1.0
CG E:GLU63 4.2 63.5 1.0
CB E:GLU63 4.3 63.5 1.0
CG E:GLU28 4.6 60.1 1.0
CG1 E:VAL111 4.6 58.8 1.0
N E:GLU63 4.9 63.5 1.0
CD E:GLN142 4.9 59.9 1.0
O E:GLU63 4.9 63.5 1.0
CA E:HIS66 4.9 62.8 1.0

Iron binding site 6 out of 24 in 7u5l

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Iron binding site 6 out of 24 in the Cryo-Em Structure of Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em Structure of Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:75.0
occ:1.00
 ND1 F:HIS66 1.7 62.8 1.0
OE1 F:GLU63 2.1 63.5 1.0
OE2 F:GLU28 2.4 60.1 1.0
CE1 F:HIS66 2.5 62.8 1.0
CG F:HIS66 2.9 62.8 1.0
CD F:GLU63 2.9 63.5 1.0
CD F:GLU28 3.2 60.1 1.0
OE1 F:GLU28 3.2 60.1 1.0
OE2 F:GLU63 3.3 63.5 1.0
CB F:HIS66 3.5 62.8 1.0
NE2 F:HIS66 3.6 62.8 1.0
CD2 F:HIS66 3.8 62.8 1.0
NE2 F:GLN142 3.9 59.9 1.0
CA F:GLU63 4.2 63.5 1.0
CG F:GLU63 4.2 63.5 1.0
CB F:GLU63 4.3 63.5 1.0
CG F:GLU28 4.6 60.1 1.0
CG1 F:VAL111 4.6 58.8 1.0
N F:GLU63 4.9 63.5 1.0
CD F:GLN142 4.9 59.9 1.0
O F:GLU63 4.9 63.5 1.0
CA F:HIS66 4.9 62.8 1.0

Iron binding site 7 out of 24 in 7u5l

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Iron binding site 7 out of 24 in the Cryo-Em Structure of Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryo-Em Structure of Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe201

b:75.0
occ:1.00
 ND1 G:HIS66 1.7 62.8 1.0
OE1 G:GLU63 2.1 63.5 1.0
OE2 G:GLU28 2.4 60.1 1.0
CE1 G:HIS66 2.5 62.8 1.0
CG G:HIS66 2.9 62.8 1.0
CD G:GLU63 2.9 63.5 1.0
CD G:GLU28 3.2 60.1 1.0
OE1 G:GLU28 3.2 60.1 1.0
OE2 G:GLU63 3.3 63.5 1.0
CB G:HIS66 3.5 62.8 1.0
NE2 G:HIS66 3.6 62.8 1.0
CD2 G:HIS66 3.8 62.8 1.0
NE2 G:GLN142 3.9 59.9 1.0
CA G:GLU63 4.2 63.5 1.0
CG G:GLU63 4.2 63.5 1.0
CB G:GLU63 4.3 63.5 1.0
CG G:GLU28 4.6 60.1 1.0
CG1 G:VAL111 4.6 58.8 1.0
N G:GLU63 4.9 63.5 1.0
CD G:GLN142 4.9 59.9 1.0
O G:GLU63 4.9 63.5 1.0
CA G:HIS66 4.9 62.8 1.0

Iron binding site 8 out of 24 in 7u5l

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Iron binding site 8 out of 24 in the Cryo-Em Structure of Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryo-Em Structure of Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe201

b:75.0
occ:1.00
 ND1 H:HIS66 1.7 62.8 1.0
OE1 H:GLU63 2.1 63.5 1.0
OE2 H:GLU28 2.4 60.1 1.0
CE1 H:HIS66 2.5 62.8 1.0
CG H:HIS66 2.9 62.8 1.0
CD H:GLU63 2.9 63.5 1.0
CD H:GLU28 3.2 60.1 1.0
OE1 H:GLU28 3.2 60.1 1.0
OE2 H:GLU63 3.3 63.5 1.0
CB H:HIS66 3.5 62.8 1.0
NE2 H:HIS66 3.6 62.8 1.0
CD2 H:HIS66 3.8 62.8 1.0
NE2 H:GLN142 3.9 59.9 1.0
CA H:GLU63 4.2 63.5 1.0
CG H:GLU63 4.2 63.5 1.0
CB H:GLU63 4.3 63.5 1.0
CG H:GLU28 4.6 60.1 1.0
CG1 H:VAL111 4.6 58.8 1.0
N H:GLU63 4.9 63.5 1.0
CD H:GLN142 4.9 59.9 1.0
O H:GLU63 4.9 63.5 1.0
CA H:HIS66 4.9 62.8 1.0

Iron binding site 9 out of 24 in 7u5l

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Iron binding site 9 out of 24 in the Cryo-Em Structure of Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cryo-Em Structure of Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe201

b:75.0
occ:1.00
 ND1 I:HIS66 1.7 62.8 1.0
OE1 I:GLU63 2.1 63.5 1.0
OE2 I:GLU28 2.4 60.1 1.0
CE1 I:HIS66 2.5 62.8 1.0
CG I:HIS66 2.9 62.8 1.0
CD I:GLU63 2.9 63.5 1.0
CD I:GLU28 3.2 60.1 1.0
OE1 I:GLU28 3.2 60.1 1.0
OE2 I:GLU63 3.3 63.5 1.0
CB I:HIS66 3.5 62.8 1.0
NE2 I:HIS66 3.6 62.8 1.0
CD2 I:HIS66 3.8 62.8 1.0
NE2 I:GLN142 3.9 59.9 1.0
CA I:GLU63 4.2 63.5 1.0
CG I:GLU63 4.2 63.5 1.0
CB I:GLU63 4.3 63.5 1.0
CG I:GLU28 4.6 60.1 1.0
CG1 I:VAL111 4.6 58.8 1.0
N I:GLU63 4.9 63.5 1.0
CD I:GLN142 4.9 59.9 1.0
O I:GLU63 4.9 63.5 1.0
CA I:HIS66 4.9 62.8 1.0

Iron binding site 10 out of 24 in 7u5l

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Iron binding site 10 out of 24 in the Cryo-Em Structure of Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cryo-Em Structure of Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe201

b:75.0
occ:1.00
 ND1 J:HIS66 1.7 62.8 1.0
OE1 J:GLU63 2.1 63.5 1.0
OE2 J:GLU28 2.4 60.1 1.0
CE1 J:HIS66 2.5 62.8 1.0
CG J:HIS66 2.9 62.8 1.0
CD J:GLU63 2.9 63.5 1.0
CD J:GLU28 3.2 60.1 1.0
OE1 J:GLU28 3.2 60.1 1.0
OE2 J:GLU63 3.3 63.5 1.0
CB J:HIS66 3.5 62.8 1.0
NE2 J:HIS66 3.6 62.8 1.0
CD2 J:HIS66 3.8 62.8 1.0
NE2 J:GLN142 3.9 59.9 1.0
CA J:GLU63 4.2 63.5 1.0
CG J:GLU63 4.2 63.5 1.0
CB J:GLU63 4.3 63.5 1.0
CG J:GLU28 4.6 60.1 1.0
CG1 J:VAL111 4.6 58.8 1.0
N J:GLU63 4.9 63.5 1.0
CD J:GLN142 4.9 59.9 1.0
O J:GLU63 4.9 63.5 1.0
CA J:HIS66 4.9 62.8 1.0

Reference:

C.E.Morgan, M.Miyagi, M.Golczak, E.W.Yu. Towards Structural-Omics of the Bovine Retinal Pigment Epithelium Cell Rep 2022.
ISSN: ESSN 2211-1247
DOI: 10.1016/J.CELREP.2022.111876
Page generated: Wed Apr 5 05:24:57 2023

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